Single-cell spatial transcriptomics of formalin-fixed, paraffin-embedded biopsies reveals colitis-associated cell networks
Authors:
- Elvira MennilloElvira Mennillo
- Madison L. LotsteinMadison L. Lotstein
- Gyehyun LeeGyehyun Lee
- Julian H. HouJulian H. Hou
- Vrinda JohriVrinda Johri
- Donna E. LeetDonna E. Leet
- Christina A. EkstrandChristina A. Ekstrand
- Jessica TsuiJessica Tsui
- Jun Yan HeJun Yan He
- Uma MahadevanUma Mahadevan
- Walter L. EckalbarWalter L. Eckalbar
- Ryan M. GillRyan M. Gill
Open Access
- 9 June 2026
- journal article
- Published by American Society for Clinical Investigation in Journal of Clinical Investigation
- Vol. 136 (14)
Abstract
Imaging-based single-cell spatial transcriptomics (iSCST) on formalin-fixed, paraffin-embedded (FFPE) tissue enables comprehensive analysis of archived specimens while preserving spatial context, critical to an understanding of ulcerative colitis (UC) pathology. Here, we deployed a robust framework for applying iSCST to clinical FFPE mucosal biopsies from patients with UC, immune checkpoint inhibitor-induced (ICI) colitis and healthy controls. iSCST using custom Xenium gene panels enabled precise detection of diverse cell subsets and disease-specific genes. We mapped transcriptionally distinct fibroblast subsets within mucosal niches, including inflammation-associated fibroblasts (IAFs), and identified colitis-specific neighborhoods formed by IAFs, monocytes, and neutrophils. Transcriptional signatures and spatial neighborhoods uncovered through iSCST were associated with vedolizumab (VDZ) response, with non-responders exhibiting either an innate IAF-monocyte-neutrophil signature or adaptive gut-associated lymphoid tissue (GALT) signature, while responders showed enrichment of an epithelial cellular neighborhood. These signatures were validated in an internal and an external dataset, supporting the existence of two distinct archetypes of treatment resistance to VDZ in UC. This iSCST framework provides a powerful approach for analyzing FFPE tissues, offering insights into colitis-associated cellular networks and identifying biomarkers to enhance patient risk stratification in routine clinical workflows.Keywords
Funding Information
- NIH (R01DK14167)
- NIH (U01DE028891-01A1)
- NIH (R01AI093615-11)
- NIH (R01DK103735)
- NIH (P30AR070155-05)
- NIH (U01AI168390)
- NIH (R01AI170239)
- NIH (P30 AI027763-31)
- NIH (R01DE032033)
- NIH (R35 CA24244)
- NIH (R01 HL181372)
- NIH (R01 HL175312)
- NIH (R35 HL171251)
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